Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012482.1 Kokia drynarioides strain JFW-HI SEQ_127486, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5909
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:48 original size:20 final size:20
Alignment explanation
Indices: 16--54 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
6 TACCTCAAAC
16 CCCAAACATTTTTATTTTTCT
1 CCCAAACATTTTT-TTTTTCT
37 CCCAAA-ATTTTTTTTTTC
1 CCCAAACATTTTTTTTTTC
55 CCACTTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (20 bp):
CCCAAACATTTTTTTTTTCT
Found at i:245 original size:30 final size:29
Alignment explanation
Indices: 202--259 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
192 ATTTTTTATT
202 TTTCCTCAAAACTTTTAC-TCCCTCTCAC
1 TTTCCTCAAAACTTTTACTTCCCTCTCAC
230 TTTCCTCTTAAAACTTTTACTTCCCTCTCA
1 TTTCCTC--AAAACTTTTACTTCCCTCTCA
260 TCTCCCCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 7 0.26
30 11 0.41
31 9 0.33
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTCCTCAAAACTTTTACTTCCCTCTCAC
Found at i:1959 original size:16 final size:17
Alignment explanation
Indices: 1938--1981 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1928 AATTATAATT
1938 TTTTAAATAAAA-ATAA
1 TTTTAAATAAAATATAA
* *
1954 TTTTAATTAAAATATTA
1 TTTTAAATAAAATATAA
1971 TTTT-AATAAAA
1 TTTTAAATAAAA
1982 CACTTAGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAATAAAATATAA
Found at i:3704 original size:23 final size:23
Alignment explanation
Indices: 3633--3796 Score: 111
Period size: 23 Copynumber: 7.0 Consensus size: 23
3623 AAGTACTTAA
* *
3633 CAGTAAGCACACAAGTGCTGCGGAAA
1 CAGTAAGCACACAA-AG-TGC-GAAT
*
3659 CAGTAAGCACACACAA-TG-TAAT
1 CAGTAAGCACACA-AAGTGCGAAT
3681 CCAGTAAGCACACAAAGTGC-AAT
1 -CAGTAAGCACACAAAGTGCGAAT
* * * *
3704 CAGT-AGACGCACATAGCGCAAAT
1 CAGTAAG-CACACAAAGTGCGAAT
* * * *
3727 CAATAGGCACACAAGGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAT
* *
3750 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAT
*
3773 CAGTAAGCACACATAGTGCTGAAT
1 CAGTAAGCACACAAAGTGC-GAAT
3797 TTTCCTTAAT
Statistics
Matches: 109, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
21 2 0.02
22 17 0.16
23 70 0.64
24 6 0.06
26 13 0.12
27 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGCGAAT
Found at i:5234 original size:10 final size:11
Alignment explanation
Indices: 5205--5233 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5195 TCAGTCTCTA
5205 ATAATTTTTCT
1 ATAATTTTTCT
5216 A-AATTTTTCT
1 ATAATTTTTCT
5226 ATAATTTT
1 ATAATTTT
5234 CCAAAGTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:5537 original size:10 final size:11
Alignment explanation
Indices: 5508--5536 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5498 TCAGTCTCTA
5508 ATAATTTTTCT
1 ATAATTTTTCT
5519 A-AATTTTTCT
1 ATAATTTTTCT
5529 ATAATTTT
1 ATAATTTT
5537 CCAAAGTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATTTTTCT
Done.